Modified SLD profiles.

buildScript.m

@@ -16,7 +16,7 @@
 
 compilePath = fullfile(root,'compile','customWrapper');
 cd(compilePath);
-wrapperMexBuild;
+%wrapperMexBuild;
 
 % Return to RAT root directory
 cd(thisPath);

targetFunctions/common/makeSLDProfiles/makeSLDProfile.m

@@ -1,54 +1,76 @@
-function SLDProfile = makeSLDProfile(bulkIn,bulkOut,layers,ssub,nrepeats)
+function SLD = makeSLDProfile(bulkIn,bulkOut,layers,lastRough,nRepeats)
 
-numberOfLayers = size(layers,1);
+bulkIn = bulkIn * 1e6;
+bulkOut = bulkOut * 1e6;
 
-if numberOfLayers>0
+if size(layers,1) > 0
+ % Make a z range for the profile...
+ % Find the maximum thickness, including any long roughness tail on final layer...
  totalThickness = sum(layers(:,1));
- totalRange = (totalThickness*nrepeats) + 150;
- x = 0:totalRange;
- Lays = zeros(length(x),(numberOfLayers*nrepeats)+2);
- boxCen = 0;
- boxWidth = 100;
-
- roughnessValues = layers(:,3)';
- roughnessValues(end+1) = ssub;
-
- nextLayerRoughness = roughnessValues(1);
- airBox = asymconvstep(x,boxWidth,boxCen,nextLayerRoughness,nextLayerRoughness,bulkIn);
- lastBoxEdge = boxCen + (0.5 * boxWidth);
-
- for n = 1:nrepeats
- for i = 1:numberOfLayers
- layerThickness = layers(i,1);
- layerSLD = layers(i,2);
- layerRoughness = roughnessValues(i);
- nextLayerRoughness = roughnessValues(i+1);
- thisBoxCentre = lastBoxEdge + (0.5 * layerThickness);
- thisBox = asymconvstep(x,layerThickness,thisBoxCentre,layerRoughness,nextLayerRoughness,layerSLD);
- Lays(:,i+(numberOfLayers*(n-1))) = thisBox;
- lastBoxEdge = thisBoxCentre + (0.5 * layerThickness);
+ outerLayerCentre = totalThickness - (layers(end,1)/2);
+
+ % Find the point which covers 99% of the outer error function..
+ outerLayerTailLim = (erfcinv(0.01) * sqrt(2) * layers(end,3)) + outerLayerCentre;
+
+ % We need to make sure the total SLD range includes this...
+ outerLayerTailExtension = outerLayerTailLim - outerLayerCentre;
+ totalRange = ((totalThickness + outerLayerTailExtension)*nRepeats);
+
+ % Add some extra range at the end for bulk_out...
+ totalRange = totalRange + 100;
+ z = 0:totalRange;
+
+ % Scale the SLDs...
+ layers(:,2) = layers(:,2) * 1e6;
+
+ % Repeat the stack according to 'nRepeats'...
+ layers = repmat(layers,nRepeats,1);
+
+ % Add an aditional 'layer' for the transition to bulk out...
+ outLayer = [0 bulkOut lastRough];
+ layers = [layers; outLayer];
+
+ % Pre-definitions....
+ nLayers = size(layers,1);
+ allFuncs = zeros(length(z),nLayers);
+ alpha = zeros(1,nLayers);
+
+ lastLayerSLD = bulkIn;
+ thisPos = 50;
+
+ % Make the profile by adding an error function for each interface (we
+ % use 'normcdf' because it scales more easily than 'erf'...)
+ for i = 1:nLayers
+ nextRough = layers(i,3);
+ nextLayerSLD = layers(i,2);
+ diff = nextLayerSLD - lastLayerSLD;
+
+ thisFun = normcdf(z,thisPos,nextRough);
+ if diff < 0
+ thisFun = -thisFun;
  end
- end
 
- layerRoughness = nextLayerRoughness;
- layerThickness = (x(end)-lastBoxEdge)*2;
- layerSLD = bulkOut;
- nextLayerRoughness = ssub;
- thisBoxCentre = x(end);
- Lays(:,(numberOfLayers*nrepeats)+1) = asymconvstep(x,layerThickness,thisBoxCentre,layerRoughness,nextLayerRoughness,layerSLD);
-
- Lays(:,(numberOfLayers*nrepeats)+2) = airBox;
- SLD = sum(Lays,2);
+ allFuncs(:,i) = thisFun(:);
+ alpha(i) = abs(diff);
+ thisPos = layers(i,1) + thisPos;
+ lastLayerSLD = nextLayerSLD;
+ end
+ totalFuncs = allFuncs.* alpha;
+ total = sum(totalFuncs,2);
 else
- x = 0:100;
- subsBoxCen = max(x);
- airBoxCen = 0;
- widths = max(x);
- airBox = asymconvstep(x,widths,airBoxCen,ssub,ssub,bulkIn);
- subBox = asymconvstep(x,widths,subsBoxCen,ssub,ssub,bulkOut);
- SLD = airBox + subBox;
+ % If we have no layers (i.e. just a bare interface), we only need one
+ % cdf...
+ z = 0:100;
+ pos = 50;
+ diff = bulkOut - bulkIn;
+ thisFun = normcdf(z,pos,lastRough);
+ if diff < 1
+ thisFun = -thisFun;
+ end
+ total = thisFun * abs(diff);
 end
 
-SLDProfile = [x(:), SLD(:)];
+total = (total + bulkIn) * 1e-6;
+SLD = [z(:) total(:)];
 
-end
+end

utilities/plotting/plotRefSLD.m

@@ -43,7 +43,66 @@ function plotRefSLD(project, result, options)
  data.subRoughs = result.contrastParams.subRoughs;
  data.resample = projectStruct.resample;
  data.contrastNames = projectStruct.names.contrasts;
+
+ % If we have air/substrate geometry, modify the SLD profiles slightly
+ % so that the substrates line up (for custom XY the user does this
+ % themselves)...
+ if strcmpi(projectStruct.geometry,'air/substrate') && ~strcmpi(projectStruct.modelType,'custom xy')
+ data = alignALProfiles(data);
+ end
 
  plotRefSLDHelper(data, false, options.linearX, options.q4, options.showErrorBar, ...
  options.showGrid, options.showLegend, options.shiftValue);
 end
+
+
+function data = alignALProfiles(data)
+% Aligns the A/L SLD profiles so that the substrates line up by padding the
+% start of any shorter than the longest profile..
+
+% Get the sld profiles out of data
+slds = data.sldProfiles;
+resamLays = data.resampledLayers;
+
+% Find the length of the longest profile...
+f = @(x)size(x{:},1);
+lengths = arrayfun(f,slds);
+maxPos = find(lengths == max(lengths));
+
+% If maxPos is an array we have many of equal (leng) length.
+% We can just pick one of them...
+if length(maxPos) > 1
+ maxPos = maxPos(1);
+end
+
+maxLen = lengths(maxPos);
+max_XValue = slds{maxPos}(end,1);
+
+% Get the longest profile...
+max_X = slds{maxPos}(:,1);
+
+% Pad the start of any profiles that are shorter than this
+for i = 1:length(slds)
+ thisSLD = slds{i};
+ thisLen = size(thisSLD,1);
+ if thisLen < maxLen
+ diffLen = maxLen - thisLen;
+ pad = zeros(diffLen,1);
+ newY = [pad ; thisSLD(:,2)];
+ slds{i} = [max_X(:,1) newY(:)];
+
+ % For resampled layers, the pad is just one big layer at the start
+ thisResam = resamLays{i};
+ if ~all(thisResam,'All') % not all zeros
+ totLength = sum(thisResam(:,1));
+ padLength = max_XValue - totLength;
+ resamPad = [padLength 0 0];
+ resamLays{i} = [resamPad ; thisResam]; 
+ end
+ end
+end
+
+data.sldProfiles = slds;
+data.resampledLayers = resamLays;
+
+end